Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 26
Found at i:1942308 original size:20 final size:22
Alignment explanation
Indices: 1942283--1942340 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1942273 TTCCCCTTGA
1942283 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
1942303 AGTGCATCAATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1942326 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1942341 GTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1946166 original size:13 final size:14
Alignment explanation
Indices: 1946148--1946178 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1946138 GTATCATATT
1946148 TCACATA-TTCATA
1 TCACATAGTTCATA
1946161 TCACATAGTTCATA
1 TCACATAGTTCATA
1946175 TCAC
1 TCAC
1946179 TTGCATGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:1946687 original size:20 final size:22
Alignment explanation
Indices: 1946662--1946719 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1946652 TTCCCCTTGA
1946662 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1946682 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1946705 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1946720 CTACCTATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1949164 original size:20 final size:21
Alignment explanation
Indices: 1949139--1949205 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
1949129 TTGTGCTTAA
1949139 TGCATCGATACACC-TAACA-G
1 TGCATCGATACACCTTAA-ATG
*
1949159 TGCATCGATGCATCCTTAAATG
1 TGCATCGATACA-CCTTAAATG
* *
1949181 TGCATCGATACACCATAAAGG
1 TGCATCGATACACCTTAAATG
1949202 TGCA
1 TGCA
1949206 CTGATGCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.28
21 14 0.35
22 15 0.38
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTAAATG
Found at i:1956340 original size:18 final size:17
Alignment explanation
Indices: 1956319--1956353 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1956309 TCCGTTATAT
*
1956319 TTTTATTTTTATTTTTTC
1 TTTTATTATT-TTTTTTC
1956337 TTTTATTATTTTTTTTC
1 TTTTATTATTTTTTTTC
1956354 CGATTAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTATTATTTTTTTTC
Found at i:1957214 original size:21 final size:18
Alignment explanation
Indices: 1957172--1957237 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
1957162 ATTCTCCATC
*
1957172 GAAAAAAAAATGTTGAAT
1 GAAAAAAAAATGTTGAAA
1957190 GAAAAAAAAAGCTGTTCGAAA
1 GAAAAAAAAA--TGTT-GAAA
**
1957211 GAAAAAGAAAA-CATGAAA
1 GAAAAA-AAAATGTTGAAA
1957229 GAAAAAAAA
1 GAAAAAAAA
1957238 TAGAAAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 3 0.07
18 20 0.49
19 1 0.02
20 4 0.10
21 9 0.22
22 4 0.10
ACGTcount: A:0.67, C:0.05, G:0.17, T:0.12
Consensus pattern (18 bp):
GAAAAAAAAATGTTGAAA
Found at i:1960984 original size:18 final size:18
Alignment explanation
Indices: 1960961--1960996 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1960951 AGGGATTTAC
1960961 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
**
1960979 AGTGGTTTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1960997 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1961006 original size:23 final size:23
Alignment explanation
Indices: 1960976--1961051 Score: 91
Period size: 23 Copynumber: 3.2 Consensus size: 23
1960966 TCCTTCGGGA
*
1960976 CATAGTGGTTTTTCGGGACATTT
1 CATAGTGGTCTTTCGGGACATTT
1960999 CATAGTGGTCCTTT-GGGACATTT
1 CATAGTGGT-CTTTCGGGACATTT
* *
1961022 CATAGTAGTCCTTCGGGACAAATTT
1 CATAGTGGTCTTTCGGGAC--ATTT
1961047 CATAG
1 CATAG
1961052 CCCCTAGTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.07
23 31 0.67
24 3 0.07
25 9 0.20
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (23 bp):
CATAGTGGTCTTTCGGGACATTT
Found at i:1969858 original size:24 final size:24
Alignment explanation
Indices: 1969829--1969887 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
1969819 AATTAGAAGT
1969829 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
1969853 TCAATTGAAGCCTAAAATTTGAGC
1 TCAATTGAAGCCTAAAATTTGAGC
1969877 TCAATTGAAGC
1 TCAATTGAAGC
1969888 GAAAGAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
TCAATTGAAGCCTAAAATTTGAGC
Found at i:1971385 original size:22 final size:22
Alignment explanation
Indices: 1971357--1971431 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
1971347 TTGAAAATCG
* *
1971357 CGTTGCGATAGCCTACAGTTGT
1 CGTTACGATAGACTACAGTTGT
*
1971379 CGTTGCGATAGACTACAGTTGT
1 CGTTACGATAGACTACAGTTGT
* *
1971401 TGTTACGATA-ATCTATAGTTGT
1 CGTTACGATAGA-CTACAGTTGT
1971423 CGTTACGAT
1 CGTTACGAT
1971432 TTTGCAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (22 bp):
CGTTACGATAGACTACAGTTGT
Found at i:1971687 original size:41 final size:40
Alignment explanation
Indices: 1971613--1971766 Score: 173
Period size: 42 Copynumber: 3.6 Consensus size: 40
1971603 CAACGAATTT
*
1971613 TCGCAACGAATTTGTAAACTATCGCAACAACAACTGTAGACTA
1 TCGCAACGAATTTG-AAA--ATCGCAACGACAACTGTAGACTA
1971656 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTT-GAAAATCGCAACGACAACTGTAGACTA
* * * *
1971697 TCGCAACGCGAAATGGAAAATCGCAACGATAACCGTAGACTA
1 TCGCAA--CGAATTTGAAAATCGCAACGACAACTGTAGACTA
* *
1971739 TCGCAACGCGAAATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGAAAATCGCAACG
1971767 CGATTTTCAA
Statistics
Matches: 103, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
41 28 0.27
42 53 0.51
43 21 0.20
44 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (40 bp):
TCGCAACGAATTTGAAAATCGCAACGACAACTGTAGACTA
Found at i:1971704 original size:22 final size:22
Alignment explanation
Indices: 1971625--1971746 Score: 103
Period size: 22 Copynumber: 5.8 Consensus size: 22
1971615 GCAACGAATT
* *
1971625 TGTAAACTATCGCAACAACAAC
1 TGTAGACTATCGCAACGACAAC
1971647 TGTAGACTATCGCAACG--AA-
1 TGTAGACTATCGCAACGACAAC
* **
1971666 TTTAGAAAATCGCAACGACAAC
1 TGTAGACTATCGCAACGACAAC
*
1971688 TGTAGACTATCGCAACG-CGAAA
1 TGTAGACTATCGCAACGAC-AAC
** *
1971710 TG--GAAAATCGCAACGATAAC
1 TGTAGACTATCGCAACGACAAC
*
1971730 CGTAGACTATCGCAACG
1 TGTAGACTATCGCAACG
1971747 CGAAATGGAA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
19 14 0.18
20 16 0.21
21 3 0.04
22 44 0.57
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
TGTAGACTATCGCAACGACAAC
Found at i:1971721 original size:20 final size:20
Alignment explanation
Indices: 1971696--1971769 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1971686 ACTGTAGACT
1971696 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** * * **
1971716 ATCGCAACGATAACCGTAGACT
1 ATCGCAACGCGAA--ATGGAAA
1971738 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1971758 ATCGCAACGCGA
1 ATCGCAACGCGA
1971770 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
20 26 0.65
22 14 0.35
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1971735 original size:42 final size:42
Alignment explanation
Indices: 1971633--1971766 Score: 200
Period size: 42 Copynumber: 3.2 Consensus size: 42
1971623 TTTGTAAACT
* * *
1971633 ATCGCAACAACAACTGTAGACTATCGCAA--CGAATTTAGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAA-ATGGAAA
1971674 ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAA
* *
1971716 ATCGCAACGATAACCGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAA
1971758 ATCGCAACG
1 ATCGCAACG
1971767 CGATTTTCAA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
41 28 0.33
42 54 0.63
43 4 0.05
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (42 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:1971780 original size:83 final size:83
Alignment explanation
Indices: 1971633--1971794 Score: 195
Period size: 83 Copynumber: 2.0 Consensus size: 83
1971623 TTTGTAAACT
* *
1971633 ATCGCAACAACAACTGTAGACTATCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTAT
1 ATCGCAACAACAACCGTAGACTATCGCAACGAATATAGAAAATCGCAACGACAACTGTAGACTAT
*
1971698 CGCAACGCGAAATGGAAA
66 CGCAACACGAAATGGAAA
* * * * * *
1971716 ATCGCAACGATAACCGTAGACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA-AC
1 ATCGCAACAACAACCGTAGACTATCGCAA--CGAATATAGAAAATCGCAACGACAACTGT-AGAC
1971778 TATCGCAACACGAAATG
63 TATCGCAACACGAAATG
1971795 CAATGCGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
83 48 0.72
84 15 0.22
85 4 0.06
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (83 bp):
ATCGCAACAACAACCGTAGACTATCGCAACGAATATAGAAAATCGCAACGACAACTGTAGACTAT
CGCAACACGAAATGGAAA
Found at i:1971974 original size:13 final size:13
Alignment explanation
Indices: 1971956--1971986 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1971946 TAACTTCATT
1971956 TTGAACTGAAAAA
1 TTGAACTGAAAAA
1971969 TTGAACTGAAAAA
1 TTGAACTGAAAAA
1971982 TTGAA
1 TTGAA
1971987 GAGAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (13 bp):
TTGAACTGAAAAA
Found at i:1976105 original size:29 final size:29
Alignment explanation
Indices: 1976063--1976148 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
1976053 AGTGTTGGCC
**
1976063 GTAGGTCGCCATGC-CTTCCGGTCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGAGACCTT
1976092 GTAGGTCGCCATGCACTCCGGGAGACCTT
1 GTAGGTCGCCATGCACTCCGGGAGACCTT
* * *
1976121 ATAGGTCGCCATACACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGAGACCT
1976149 ACCCTTGCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 50 0.98
30 1 0.02
ACGTcount: A:0.16, C:0.34, G:0.28, T:0.22
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGAGACCTT
Found at i:1976309 original size:23 final size:23
Alignment explanation
Indices: 1976280--1976339 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1976270 CTCGGCTGCC
* *
1976280 CTCGGATTCCCTCGCATATCTCG
1 CTCGGATGCCCTCGCATAGCTCG
1976303 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* * *
1976326 TTTGGATGGCCTCG
1 CTCGGATGCCCTCG
1976340 GATGCTCTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.12, C:0.35, G:0.25, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:1976354 original size:20 final size:20
Alignment explanation
Indices: 1976329--1976380 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1976319 TAGCTCGTTT
1976329 GGATGGCCTCGGATGCTCTC
1 GGATGGCCTCGGATGCTCTC
*
1976349 GGATGGCCTCTGATGCTCTC
1 GGATGGCCTCGGATGCTCTC
*
1976369 GGATAGCCTCGG
1 GGATGGCCTCGG
1976381 TCGGATGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.29, G:0.35, T:0.25
Consensus pattern (20 bp):
GGATGGCCTCGGATGCTCTC
Found at i:1976379 original size:10 final size:9
Alignment explanation
Indices: 1976329--1976380 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 9
1976319 TAGCTCGTTT
1976329 GGATGGCCTC
1 GGAT-GCCTC
1976339 GGATGCTCTC
1 GGATGC-CTC
1976349 GGATGGCCTC
1 GGAT-GCCTC
*
1976359 TGATGCTCTC
1 GGATGC-CTC
1976369 GGATAGCCTC
1 GGAT-GCCTC
1976379 GG
1 GG
1976381 TCGGATGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 28 0.78
11 4 0.11
ACGTcount: A:0.12, C:0.29, G:0.35, T:0.25
Consensus pattern (9 bp):
GGATGCCTC
Found at i:1979542 original size:3 final size:3
Alignment explanation
Indices: 1979475--1979529 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
1979465 TAAAATATGT
**
1979475 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ACG ATA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1979521 ATA ATA ATA
1 ATA ATA ATA
1979530 TTTTTAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1979795 original size:40 final size:41
Alignment explanation
Indices: 1979687--1979796 Score: 125
Period size: 43 Copynumber: 2.7 Consensus size: 41
1979677 TTTGTGTTGG
* *
1979687 GGGACGACACGGCTCATACGCGATGAAGAGGTCTGGTCGTCTAA
1 GGGATGACACGGCTCATACGCGATGAAGAGATCTGGTCG--T-A
* * *
1979731 GGG-TGACACGGCTCCTACGTGATGAGGAGATCTGGTCG-A
1 GGGATGACACGGCTCATACGCGATGAAGAGATCTGGTCGTA
*
1979770 GGGATGACACTGCTCATACGCGATGAA
1 GGGATGACACGGCTCATACGCGATGAA
1979797 AAGTTTTTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 4 0.07
40 19 0.34
43 30 0.54
44 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.35, T:0.19
Consensus pattern (41 bp):
GGGATGACACGGCTCATACGCGATGAAGAGATCTGGTCGTA
Found at i:1980054 original size:133 final size:133
Alignment explanation
Indices: 1979700--1980083 Score: 461
Period size: 135 Copynumber: 2.9 Consensus size: 133
1979690 ACGACACGGC
* * * ** *
1979700 TCATACGCGATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTG
1 TCATACGCGATGAGGACGACTGGTTATCT-AGGGTGACACGGCTCCTACGTGATGAGGAGGTCTG
* * * *
1979765 GTCGAGGG-ATGACAC-TGCTCATACGCGATGAAAAGTTTTTGGCCATCTTTAGGAAAGATGATA
65 GTCG-GGGAATGACACGT-CTCATACGTGATGAAGAG-TTCTGGCCATCTTTAAGAAAGATGATA
1979828 ACTCGGT
127 ACTCGGT
* *
1979835 TCATACGCGATGAGGACGACTGGTTATTTATGGGTGACACGGCTCCTACGTGATGAGGAGGGCTG
1 TCATACGCGATGAGGACGACTGGTTATCTA-GGGTGACACGGCTCCTACGTGATGAGGAGGTCTG
* * * *
1979900 GTCAGGGAATGACACGACTCATACATGATGAAGAGTTCTGGCCATCTTTAAGAAGGGA-GATAAC
65 GTCGGGGAATGACACGTCTCATACGTGATGAAGAGTTCTGGCCATCTTTAAGAA-AGATGATAAC
1979964 AT-GGT
129 -TCGGT
* * * * *
1979969 TCCTACGTGATGAGGACTACTGGTTATCTAGGGTGACACGACTCCTACGCGATGAGGAGGTCTGG
1 TCATACGCGATGAGGACGACTGGTTATCTAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGG
* *
1980034 TCGGGGAAGGGCACGTCTCATACGTGATGAAGAGTTCTTGGCCATCTTTA
66 TCGGGGAATGACACGTCTCATACGTGATGAAGAGTTC-TGGCCATCTTTA
1980084 GGGATTATGG
Statistics
Matches: 215, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
133 64 0.30
134 68 0.32
135 83 0.39
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (133 bp):
TCATACGCGATGAGGACGACTGGTTATCTAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGG
TCGGGGAATGACACGTCTCATACGTGATGAAGAGTTCTGGCCATCTTTAAGAAAGATGATAACTC
GGT
Found at i:1980133 original size:28 final size:30
Alignment explanation
Indices: 1980089--1980160 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
1980079 CTTTAGGGAT
*
1980089 TATG-GTTTCAAGAGAAATCA-ACTCAAAGA
1 TATGTGTTTCAAAAGAAA-CATACTCAAAGA
1980118 T-T-TGTTTCAAAAGAAACATACTCAAAGA
1 TATGTGTTTCAAAAGAAACATACTCAAAGA
1980146 TAATGTGTTTCAAAA
1 T-ATGTGTTTCAAAA
1980161 TCAACTGTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 2 0.05
28 23 0.62
29 1 0.03
30 1 0.03
31 10 0.27
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (30 bp):
TATGTGTTTCAAAAGAAACATACTCAAAGA
Found at i:1980553 original size:66 final size:66
Alignment explanation
Indices: 1980466--1980686 Score: 211
Period size: 66 Copynumber: 3.3 Consensus size: 66
1980456 AAGTGAGGCG
* * * *
1980466 AAATTTGTTTCAAAGGAAACAATCTCAAAGGTTGGTT-TTTCATTAGAAACTGTCTCAA-GAGAG
1 AAATTTGTTTTAAA-GAAACAATCTCAAAGGTTGGTTGTTTCATAAGAAACAGTCTCAAGGA-AA
1980529 ATA
64 ATA
* *
1980532 AAATTTGTTTTTAAAGAAACAA-CTCAAAGATGATT-TTTGTTTCATGAGAAA-AGGTCTCAAGG
1 AAATTTG-TTTTAAAGAAACAATCTCAAAG--G-TTGGTTGTTTCATAAGAAACA-GTCTCAAGG
1980594 AAAATA
61 AAAATA
* * **
1980600 AGATTTGTTTTAAGAGAAACGATCTCAAA-AATGGTTGTTTCATAAGAAACAGTCTCAAGGAAAA
1 AAATTTGTTTTAA-AGAAACAATCTCAAAGGTTGGTTGTTTCATAAGAAACAGTCTCAAGGAAAA
1980664 TA
65 TA
* *
1980666 AGATTTGTTTCAAAAGAAACA
1 AAATTTGTTT-TAAAGAAACA
1980687 TACTTATAGA
Statistics
Matches: 130, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
65 8 0.06
66 59 0.45
67 18 0.14
68 37 0.28
69 8 0.06
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (66 bp):
AAATTTGTTTTAAAGAAACAATCTCAAAGGTTGGTTGTTTCATAAGAAACAGTCTCAAGGAAAAT
A
Found at i:1980683 original size:36 final size:36
Alignment explanation
Indices: 1980567--1980686 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 36
1980557 AAAGATGATT
**
1980567 TTTGTTTCATGAGAAA-AGGTCTCAAGGAAAATAAGA
1 TTTGTTTCAAAAGAAACA-GTCTCAAGGAAAATAAGA
* *
1980603 TTTGTTTTAAGAGAAAC-GATCTC-A--AAAAT--G-
1 TTTGTTTCAAAAGAAACAG-TCTCAAGGAAAATAAGA
* *
1980633 GTTGTTTCATAAGAAACAGTCTCAAGGAAAATAAGA
1 TTTGTTTCAAAAGAAACAGTCTCAAGGAAAATAAGA
1980669 TTTGTTTCAAAAGAAACA
1 TTTGTTTCAAAAGAAACA
1980687 TACTTATAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
30 17 0.25
31 3 0.04
33 10 0.15
35 3 0.04
36 34 0.51
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAAAGAAACAGTCTCAAGGAAAATAAGA
Found at i:1980890 original size:36 final size:37
Alignment explanation
Indices: 1980844--1980913 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
1980834 TCAGAGAGGA
* * *
1980844 AAAAAATGTCTCAAGCGAGAC-GAAATTTGTTTTGAG
1 AAAAAATGTCTCAAACAAGACAAAAATTTGTTTTGAG
*
1980880 AAAAATTGTCTCAAACAAGACAAAAATTTGTTTT
1 AAAAAATGTCTCAAACAAGACAAAAATTTGTTTT
1980914 AAAATTCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 18 0.62
37 11 0.38
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (37 bp):
AAAAAATGTCTCAAACAAGACAAAAATTTGTTTTGAG
Found at i:1981125 original size:36 final size:35
Alignment explanation
Indices: 1981084--1981212 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 35
1981074 AAAGGAAAAA
1981084 TGTCTCAAGCGAGACGAAATTTATTTTTCAAGAAAT
1 TGTCTCAAGCGAGAC-AAATTTATTTTTCAAGAAAT
** *
1981120 TGTCTCAAATGAGACAAAATTTGTTTTT--AGAAAAT
1 TGTCTCAAGCGAGAC-AAATTTATTTTTCAAG-AAAT
* *
1981155 TGTCTCAAGCGAGAC-AATTTTTTTTTCAAAAGAAAC
1 TGTCTCAAGCGAGACAAATTTATTTTTC--AAGAAAT
*
1981191 TGTCTCTAGCGAGACAACATTT
1 TGTCTCAAGCGAGACAA-ATTT
1981213 TGTTTCGAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
33 10 0.13
34 2 0.03
35 17 0.22
36 41 0.53
37 3 0.04
38 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTATTTTTCAAGAAAT
Found at i:1981205 original size:71 final size:71
Alignment explanation
Indices: 1981078--1981217 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 71
1981068 TATCTCAAAG
* *
1981078 GAAAAATGTCTCAAGCGAGACGAAATTTATTTTTCAAGAAATTGTCTCAAATGAGACAA-AATTT
1 GAAAAATGTCTCAAGCGAGAC-AAATTTATTTTTCAAGAAACTGTCTCAAACGAGACAACAATTT
1981142 GTTTTTA
65 GTTTTTA
* * * * *
1981149 GAAAATTGTCTCAAGCGAGAC-AATTTTTTTTTCAAAAGAAACTGTCTCTAGCGAGACAACATTT
1 GAAAAATGTCTCAAGCGAGACAAATTTATTTTTC--AAGAAACTGTCTCAAACGAGACAACAATT
1981213 TGTTT
64 TGTTT
1981218 CGAGAGAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
69 11 0.19
71 40 0.68
72 8 0.14
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (71 bp):
GAAAAATGTCTCAAGCGAGACAAATTTATTTTTCAAGAAACTGTCTCAAACGAGACAACAATTTG
TTTTTA
Found at i:1981226 original size:37 final size:36
Alignment explanation
Indices: 1981084--1981227 Score: 123
Period size: 35 Copynumber: 4.0 Consensus size: 36
1981074 AAAGGAAAAA
* *
1981084 TGTCTCAAGCGAGACGAAATTTATTTTTC-A-AGAAAT
1 TGTCTCAAGCGAGAC-AAATTT-TGTTTCAAGAGAAAC
** * ** *
1981120 TGTCTCAAATGAGACAAAATTTGTTTTTAGA-AAAT
1 TGTCTCAAGCGAGACAAATTTTGTTTCAAGAGAAAC
* * *
1981155 TGTCTCAAGCGAGACAATTTTTTTTTCAAAAGAAAC
1 TGTCTCAAGCGAGACAAATTTTGTTTCAAGAGAAAC
* *
1981191 TGTCTCTAGCGAGACAACATTTTGTTTCGAGAGAAAC
1 TGTCTCAAGCGAGACAA-ATTTTGTTTCAAGAGAAAC
1981228 AACATCAAAG
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
34 4 0.05
35 33 0.39
36 33 0.39
37 15 0.18
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAATTTTGTTTCAAGAGAAAC
Found at i:1982778 original size:15 final size:15
Alignment explanation
Indices: 1982748--1982786 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1982738 TTGTTTCTTG
*
1982748 CTTTGCTTTTTTTTCT
1 CTTTG-TTTCTTTTCT
1982764 CTTTGTTTCTTTTCT
1 CTTTGTTTCTTTTCT
*
1982779 CATTGTTT
1 CTTTGTTT
1982787 TTTCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.03, C:0.18, G:0.08, T:0.72
Consensus pattern (15 bp):
CTTTGTTTCTTTTCT
Found at i:1982791 original size:13 final size:14
Alignment explanation
Indices: 1982755--1982789 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1982745 TTGCTTTGCT
*
1982755 TTTTTTTCTCTTTG
1 TTTTTTTCTCATTG
1982769 TTTCTTTTCTCATTG
1 TTT-TTTTCTCATTG
1982784 TTTTTT
1 TTTTTT
1982790 CTTTTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTCATTG
Found at i:1985110 original size:24 final size:24
Alignment explanation
Indices: 1985083--1985139 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1985073 CATGGGGTAG
1985083 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
1985107 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
1985131 TGCATCGAT
1 TGCATCGAT
1985140 ACACTGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:1986678 original size:25 final size:25
Alignment explanation
Indices: 1986661--1986712 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1986651 TTTCATCTTT
1986661 TTATTAATATTATATTTTAGTATTA
1 TTATTAATATTATATTTTAGTATTA
* *
1986686 TTATTAATATTAT-TATTATTATTA
1 TTATTAATATTATATTTTAGTATTA
1986710 TTA
1 TTA
1986713 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATTAATATTATATTTTAGTATTA
Found at i:1986689 original size:3 final size:3
Alignment explanation
Indices: 1986661--1986712 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
1986651 TTTCATCTTT
* * *
1986661 TTA TTA ATA TTA -TA TT- TTA GTA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1986707 TTA TTA
1 TTA TTA
1986713 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1988207 original size:11 final size:11
Alignment explanation
Indices: 1988191--1988216 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1988181 TAAATTAGTA
1988191 ATTTAATTATT
1 ATTTAATTATT
1988202 ATTTAATTATT
1 ATTTAATTATT
1988213 ATTT
1 ATTT
1988217 TAGTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:1989701 original size:46 final size:49
Alignment explanation
Indices: 1989612--1989702 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 49
1989602 TTATTTTTCT
* *
1989612 TTTTTCCTAAATAAATGCATGCGAACTAAAAATCATGCAGTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGCGAACTAAAAAGCATGCAGTTAGGTTAA
*
1989661 TTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATG-AGGTTAGG
1 TTTTTCCTAAACAAATGCATGCGAACTAAAAAGCATGCA-GTTAGG
1989703 ATTTATACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
45 1 0.03
46 19 0.50
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGCGAACTAAAAAGCATGCAGTTAGGTTAA
Found at i:2008324 original size:15 final size:16
Alignment explanation
Indices: 2008304--2008333 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2008294 CCCTTTCATC
2008304 TAGAGTG-TGGGATGG
1 TAGAGTGATGGGATGG
2008319 TAGAGTGATGGGATG
1 TAGAGTGATGGGATG
2008334 ACTCTCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (16 bp):
TAGAGTGATGGGATGG
Found at i:2008729 original size:20 final size:20
Alignment explanation
Indices: 2008704--2008746 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2008694 TCTAAGAGCA
*
2008704 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
2008724 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
2008744 CAT
1 CAT
2008747 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:2010693 original size:73 final size:73
Alignment explanation
Indices: 2010574--2011048 Score: 729
Period size: 73 Copynumber: 6.5 Consensus size: 73
2010564 CTATTTCCAA
*
2010574 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
2010639 CTCAGGGT
66 CTCAGGGT
* * * *
2010647 CATCTGCAAGACCTACAGTGCATGGTGTTTTCAAAAAGCCTTCGGGAGATTTTTGATCTTAAAGT
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
2010712 CTCAGGGT
66 CTCAGGGT
* * * * *
2010720 CATCTGTAAGACCTACAATACATTG-TGTTTTCAAAAAGCCTCCGGTAGCTTTTTGATCTTAAAT
1 CATCTGTAAGACCTACAGTGCA-TGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAG
2010784 CCTCAGGGT
65 CCTCAGGGT
* * *
2010793 CATCTGTAAGACCTGCAGTGCA-GAATGTTTTCAAAAAGACTTCGGGAGCTTTTTGAAGTTTTTA
1 CATCTGTAAGACCTACAGTGCATG-ATGTTTTCAAAAAGCCTTCGGGAGCTTTTTG-A--TCTTA
2010857 AAGCCTCAGGGT
62 AAGCCTCAGGGT
* * *
2010869 CATCTGTAAGACCTACAGTGCATGATGTTTTTAAAAAGCCTTCGGGAGCTTTTTTATTTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
* *
2010934 CTCATGAT
66 CTCAGGGT
2010942 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
2011007 CTCAGGGT
66 CTCAGGGT
2011015 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
2011049 CATTTCAATC
Statistics
Matches: 363, Mismatches: 32, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.00
73 293 0.81
74 3 0.01
75 1 0.00
76 64 0.18
77 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:2010957 original size:222 final size:219
Alignment explanation
Indices: 2010574--2011048 Score: 729
Period size: 222 Copynumber: 2.2 Consensus size: 219
2010564 CTATTTCCAA
* *
2010574 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGACTTCGGGAGCTTTTTGATCTTAAAGC
*
2010639 CTCAGGGTCATCTGCAAGACCTACAGTGCATGGTGTTTTCAAAAAGCCTTCGGGAGATTTTTGAT
66 CTCAGGGTCATCTGCAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGAT
* * *
2010704 CTTAAAGTCTCAGGGTCATCTGTAAGACCTACAATACATTG-TGTTTTCAAAAAGCCTCCGGTAG
131 CTTAAAGCCTCAGGATCATCTGTAAGACCTACAATACA-TGATGTTTTCAAAAAGCCTCCGGGAG
*
2010768 CTTTTTGATCTTAAATCCTCAGGGT
195 CTTTTTGATCTTAAAGCCTCAGGGT
* *
2010793 CATCTGTAAGACCTGCAGTGCA-GAATGTTTTCAAAAAGACTTCGGGAGCTTTTTGAAGTTTTTA
1 CATCTGTAAGACCTACAGTGCATG-ATGTTTTCAAAAAGACTTCGGGAGCTTTTTG-A--TCTTA
* * *
2010857 AAGCCTCAGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTTAAAAAGCCTTCGGGAGCTTTT
62 AAGCCTCAGGGTCATCTGCAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTT
* * * * * *
2010922 TTATTTTAAAGCCTCATGATCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGG
127 TGATCTTAAAGCCTCAGGATCATCTGTAAGACCTACAATACATGATGTTTTCAAAAAGCCTCCGG
2010987 GAGCTTTTTGATCTTAAAGCCTCAGGGT
192 GAGCTTTTTGATCTTAAAGCCTCAGGGT
2011015 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
2011049 CATTTCAATC
Statistics
Matches: 231, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
218 1 0.00
219 50 0.22
220 1 0.00
221 2 0.01
222 176 0.76
223 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (219 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGACTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGTCATCTGCAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGAT
CTTAAAGCCTCAGGATCATCTGTAAGACCTACAATACATGATGTTTTCAAAAAGCCTCCGGGAGC
TTTTTGATCTTAAAGCCTCAGGGT
Found at i:2011199 original size:3 final size:3
Alignment explanation
Indices: 2011171--2011231 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
2011161 TTTCATCTTT
* *
2011171 TTA TTA ATA TTA -TA TT- TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2011217 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2011232 AATAAATTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2012735 original size:11 final size:11
Alignment explanation
Indices: 2012719--2012744 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2012709 TAAATTAGTA
2012719 ATTTAATTATT
1 ATTTAATTATT
2012730 ATTTAATTATT
1 ATTTAATTATT
2012741 ATTT
1 ATTT
2012745 TAGTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTATT
Found at i:2012834 original size:16 final size:16
Alignment explanation
Indices: 2012793--2012842 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2012783 AAAACATATA
*
2012793 TATATTTTTATTCA-TA
1 TATATTTTT-TTCATTT
*
2012809 T-TATTATTTTCATTT
1 TATATTTTTTTCATTT
*
2012824 TATATTTTTTTAATTT
1 TATATTTTTTTCATTT
2012840 TAT
1 TAT
2012843 TCATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 16 0.57
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTTTTTCATTT
Found at i:2013581 original size:21 final size:21
Alignment explanation
Indices: 2013557--2013616 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
2013547 GTCGAGGGAT
*
2013557 TATCAGTGGTCTTTCGGGACA
1 TATCAGTGGTCATTCGGGACA
* *
2013578 TATCAGTGATCCTTCGGG--A
1 TATCAGTGGTCATTCGGGACA
2013597 TAT-AGTGGTCATTCGGGACA
1 TATCAGTGGTCATTCGGGACA
2013617 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 1 0.03
21 16 0.48
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (21 bp):
TATCAGTGGTCATTCGGGACA
Found at i:2017106 original size:25 final size:23
Alignment explanation
Indices: 2017061--2017113 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
2017051 TTTTTGAAAA
*
2017061 AAAAACAATTAAATATTATTTTT
1 AAAAACAATTAAATATTATTTTG
2017084 AAAAACAATTATAACT-TTAATTTTG
1 AAAAACAATTA-AA-TATT-ATTTTG
2017109 AAAAA
1 AAAAA
2017114 TTGGGGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
24 4 0.15
25 11 0.42
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAACAATTAAATATTATTTTG
Found at i:2019577 original size:3 final size:3
Alignment explanation
Indices: 2019569--2019616 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
2019559 ATATGTAAAC
* **
2019569 TAA TAA TAA TAA TAA TAA CAA -AA TAA CGA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2019615 TA
1 TA
2019617 TTTTTAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2020098 original size:19 final size:19
Alignment explanation
Indices: 2020074--2020113 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2020064 ACTTGAGGCA
2020074 GGGATCGATCCTCACCATG
1 GGGATCGATCCTCACCATG
2020093 GGGATCGATCCTCACCATG
1 GGGATCGATCCTCACCATG
2020112 GG
1 GG
2020114 TTTAGTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (19 bp):
GGGATCGATCCTCACCATG
Found at i:2021534 original size:3 final size:3
Alignment explanation
Indices: 2021526--2021558 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2021516 TTGTCCGAGA
2021526 TAT TAT TAT TA- TAT TAT TAT T-T TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2021559 ATGTTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2021541 original size:11 final size:11
Alignment explanation
Indices: 2021525--2021558 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
2021515 TTTGTCCGAG
2021525 ATATTATTATT
1 ATATTATTATT
2021536 ATATTATTATT
1 ATATTATTATT
*
2021547 TTATTATTATT
1 ATATTATTATT
2021558 A
1 A
2021559 ATGTTAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTATTATT
Found at i:2042677 original size:21 final size:20
Alignment explanation
Indices: 2042639--2042678 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2042629 TTGTTTCTGA
* *
2042639 TTTCCCTCCTTTCCTTTTTC
1 TTTCCCTCCCTTCATTTTTC
2042659 TTTCCCTCCCTTCTATTTTT
1 TTTCCCTCCCTTC-ATTTTT
2042679 TTTGGTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTCCCTCCCTTCATTTTTC
Found at i:2042699 original size:142 final size:143
Alignment explanation
Indices: 2042525--2042805 Score: 440
Period size: 143 Copynumber: 2.0 Consensus size: 143
2042515 AGAATTTCTT
* * ** *
2042525 CCTTCTATTTTTTTCGGTGTAAGAAAAGGAAACATAAAAGAAAGCA-AAAGTGACAGTGACAGTG
1 CCTTCTATTTTTTTCGGTGAAAGAAAAGGAAACATAAAAGAAA-AAGAAAGAAAAAGTGACAGTG
* * *
2042589 A-AAATATGACAACAAATATGAAAAGCTTTGGTACTCTAGCTTGTTTCTGATTTCCCTCCTTTCC
65 ACAAAAATGACAACAAATATGAAAAGCTTTAGTACTCTAGATTGTTTCTGATTTCCCTCCTTTCC
2042653 TTTTTCTTTCCCTC
130 TTTTTCTTTCCCTC
* *
2042667 CCTTCTATTTTTTTTGGTGAAAGAAAATGAAACATAAAAGAAAAAGAAAGAAAAAGTGACAGTGA
1 CCTTCTATTTTTTTCGGTGAAAGAAAAGGAAACATAAAAGAAAAAGAAAGAAAAAGTGACAGTGA
*
2042732 CAAAAATGACAACAAATATGAAAAGCTTTAGTACTCTAGATTGTTTCTGATTTCCCTCTTTTCCT
66 CAAAAATGACAACAAATATGAAAAGCTTTAGTACTCTAGATTGTTTCTGATTTCCCTCCTTTCCT
2042797 TTTTCTTTC
131 TTTTCTTTC
2042806 TAAAATGAAT
Statistics
Matches: 126, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 1 0.01
142 56 0.44
143 69 0.55
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (143 bp):
CCTTCTATTTTTTTCGGTGAAAGAAAAGGAAACATAAAAGAAAAAGAAAGAAAAAGTGACAGTGA
CAAAAATGACAACAAATATGAAAAGCTTTAGTACTCTAGATTGTTTCTGATTTCCCTCCTTTCCT
TTTTCTTTCCCTC
Found at i:2051364 original size:6 final size:6
Alignment explanation
Indices: 2051353--2051378 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2051343 TTGTAATAAA
2051353 GCTTTT GCTTTT GCTTTT GCTTTT GC
1 GCTTTT GCTTTT GCTTTT GCTTTT GC
2051379 AATTTGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62
Consensus pattern (6 bp):
GCTTTT
Found at i:2069639 original size:36 final size:36
Alignment explanation
Indices: 2069590--2069659 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
2069580 TTGATTCCTT
2069590 TAACACTGCTGATTCATGGTTTTAGGTATGGTTTGG
1 TAACACTGCTGATTCATGGTTTTAGGTATGGTTTGG
* *
2069626 TAACACTGTTGATTCATGGTTTTGGGTATGGTTT
1 TAACACTGCTGATTCATGGTTTTAGGTATGGTTT
2069660 TAGGGGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (36 bp):
TAACACTGCTGATTCATGGTTTTAGGTATGGTTTGG
Found at i:2070449 original size:14 final size:16
Alignment explanation
Indices: 2070430--2070462 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2070420 TGTTCTAGTA
2070430 ATTTTAAAA-AA-GTT
1 ATTTTAAAACAATGTT
2070444 ATTTTAAAACAATGTT
1 ATTTTAAAACAATGTT
2070460 ATT
1 ATT
2070463 ATATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTTTAAAACAATGTT
Found at i:2072737 original size:23 final size:22
Alignment explanation
Indices: 2072711--2072753 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2072701 TATAAAAAAT
2072711 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
2072734 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
2072754 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:2083346 original size:16 final size:16
Alignment explanation
Indices: 2083327--2083378 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 16
2083317 TTTTTAATTT
2083327 AATTACTTAACTTTCA
1 AATTACTTAACTTTCA
2083343 AATTACTCTTAA-TTT--
1 AATTA--CTTAACTTTCA
2083358 AATTACTCTAACTTTCA
1 AATTACT-TAACTTTCA
2083375 AATT
1 AATT
2083379 TATTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 8 0.27
16 5 0.17
17 7 0.23
18 5 0.17
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTACTTAACTTTCA
Found at i:2083363 original size:15 final size:15
Alignment explanation
Indices: 2083320--2083366 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2083310 TAAATCTTTT
2083320 TTAATTTAATTA--C
1 TTAATTTAATTACTC
2083333 TTAACTTTCAAATTACTC
1 TTAA-TTT--AATTACTC
2083351 TTAATTTAATTACTC
1 TTAATTTAATTACTC
2083366 T
1 T
2083367 AACTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 3 0.10
15 9 0.31
16 5 0.17
17 3 0.10
18 5 0.17
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATTTAATTACTC
Found at i:2086809 original size:10 final size:10
Alignment explanation
Indices: 2086758--2086812 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
2086748 TGACATTCTT
2086758 TTTTTATTAA
1 TTTTTATTAA
* *
2086768 ATTTTATTCA
1 TTTTTATTAA
* *
2086778 CTTTAATT--
1 TTTTTATTAA
2086786 TTTTTATTATA
1 TTTTTATTA-A
2086797 TTTTTATTAA
1 TTTTTATTAA
2086807 TTTTTA
1 TTTTTA
2086813 AATATATGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 6 0.17
10 21 0.58
11 9 0.25
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATTAA
Found at i:2089442 original size:10 final size:10
Alignment explanation
Indices: 2089427--2089465 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
2089417 AAAATATATC
2089427 TATATATTTA
1 TATATATTTA
*
2089437 TTTATATTTA
1 TATATATTTA
*
2089447 TATATATATA
1 TATATATTTA
2089457 TATAATATT
1 TAT-ATATT
2089466 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATATTTA
Found at i:2090189 original size:32 final size:32
Alignment explanation
Indices: 2090149--2090230 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
2090139 TTTAATTTTG
2090149 TAAAAAAATATATATATAAATTTAAAACTT-T
1 TAAAAAAATATATATATAAATTTAAAACTTGT
* * **
2090180 TAAAGAAAATATATAAAT-ATTTTTTAACTTGT
1 TAAA-AAAATATATATATAAATTTAAAACTTGT
*
2090212 TAAAAAAATAAATATATAA
1 TAAAAAAATATATATATAA
2090231 TAAGGACAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
31 24 0.57
32 18 0.43
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (32 bp):
TAAAAAAATATATATATAAATTTAAAACTTGT
Found at i:2092061 original size:40 final size:40
Alignment explanation
Indices: 2092017--2092132 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 40
2092007 TCTCTCTCTC
2092017 TTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTA
1 TTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTA
* * * *** *
2092057 TTCT-CG--GCCTC-CTCTTTCATCAAATG--ATC-T-CT-
1 TTCTCCGATGTCTCGATCATTC-TCCTTTGCTCTCTTGCTA
2092089 -TCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTA
1 TTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTA
2092128 TTCTC
1 TTCTC
2092133 GGCCTCCTCT
Statistics
Matches: 51, Mismatches: 14, Indels: 22
0.59 0.16 0.25
Matches are distributed among these distances:
31 3 0.06
32 2 0.04
33 2 0.04
34 9 0.18
35 7 0.14
36 7 0.14
37 9 0.18
38 2 0.04
39 2 0.04
40 8 0.16
ACGTcount: A:0.11, C:0.34, G:0.11, T:0.44
Consensus pattern (40 bp):
TTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTA
Found at i:2092129 original size:71 final size:71
Alignment explanation
Indices: 2092013--2092154 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
2092003 CCATTCTCTC
2092013 TCTCTTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTATTCTCGGCCTCCTCTTTCATC
1 TCTCTTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTATTCTCGGCCTCCTCTTTCATC
2092078 AAATGA
66 AAATGA
2092084 TCTCTTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTATTCTCGGCCTCCTCTTTCATC
1 TCTCTTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTATTCTCGGCCTCCTCTTTCATC
2092149 AAATGA
66 AAATGA
2092155 ACATCTCGTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.13, C:0.34, G:0.11, T:0.42
Consensus pattern (71 bp):
TCTCTTCTCCGATGTCTCGATCATTCTCCTTTGCTCTCTTGCTATTCTCGGCCTCCTCTTTCATC
AAATGA
Found at i:2094227 original size:42 final size:42
Alignment explanation
Indices: 2094107--2094229 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
2094097 AGTATCGTTG
* * *
2094107 CTATACTTTGGCCAAGACTGTAAGATGTATTACTGACTTTTG
1 CTATACTTTGGCCGAGACTGTAAGATGTATTACTGATTTTTA
*
2094149 CTATACTTTGGCCGAGACTGTTAGATGTATTACTGATTTTTA
1 CTATACTTTGGCCGAGACTGTAAGATGTATTACTGATTTTTA
* * *
2094191 CTATACTTAGGCCGAGACTGAAAGATGTATTGCTGATTT
1 CTATACTTTGGCCGAGACTGTAAGATGTATTACTGATTT
2094230 CTAGTTCTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (42 bp):
CTATACTTTGGCCGAGACTGTAAGATGTATTACTGATTTTTA
Found at i:2098145 original size:23 final size:24
Alignment explanation
Indices: 2098096--2098146 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2098086 GTACGGTCAA
* *
2098096 ATTTTTAGTAATTTATTTTTTAGT
1 ATTTTTAGTAATTTATTTTTGAAT
2098120 ATTTTTA-T-ATTTAATTTTTGAAT
1 ATTTTTAGTAATTT-ATTTTTGAAT
2098143 ATTT
1 ATTT
2098147 AAATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 13 0.54
24 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (24 bp):
ATTTTTAGTAATTTATTTTTGAAT
Found at i:2099967 original size:23 final size:23
Alignment explanation
Indices: 2099941--2100000 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
2099931 GGGTCTATGC
*
2099941 GGTCATTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
2099964 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
2099987 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
2100001 TATATGTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:2106486 original size:23 final size:24
Alignment explanation
Indices: 2106451--2106495 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2106441 TTTAAAGGAC
2106451 TAAAAATATAATTAATTAAAATTT
1 TAAAAATATAATTAATTAAAATTT
* *
2106475 TAAAAGTA-AATTATTTAAAAT
1 TAAAAATATAATTAATTAAAAT
2106496 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAAAATATAATTAATTAAAATTT
Found at i:2106498 original size:14 final size:15
Alignment explanation
Indices: 2106467--2106503 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2106457 TATAATTAAT
2106467 TAAAAT-TTTAAAAG
1 TAAAATATTTAAAAG
*
2106481 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
2106495 TAAAATATT
1 TAAAATATT
2106504 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:2107675 original size:40 final size:40
Alignment explanation
Indices: 2107609--2107759 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
2107599 ATTTTGTAAA
* * *
2107609 TCGCAACATATAAGTCATATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
*
2107649 TCGTAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * *
2107689 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
2107729 TCGCAACGC-GATAGTCAAATTCACAACGCGA
1 TCGCAACACAGA-AGTCAAATTCGCAACGCGA
2107760 AACACAATAT
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 1 0.01
40 95 0.99
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (40 bp):
TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:2107705 original size:60 final size:60
Alignment explanation
Indices: 2107621--2107755 Score: 207
Period size: 60 Copynumber: 2.2 Consensus size: 60
2107611 GCAACATATA
* * * * * *
2107621 AGTCATATTCGCAACGCGATAGTCAAATTCGTAACACAGAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
2107681 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
*
2107741 AGTCAAATTCACAAC
1 AGTCAAATTCGCAAC
2107756 GCGAAACACA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.19
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:2107756 original size:20 final size:20
Alignment explanation
Indices: 2107621--2107759 Score: 172
Period size: 20 Copynumber: 7.0 Consensus size: 20
2107611 GCAACATATA
*
2107621 AGTCATATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
2107641 AGTCAAATTCGTAACACAGA-
1 AGTCAAATTCGCAACGC-GAT
2107661 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * *
2107681 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
* * *
2107701 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
2107721 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
*
2107741 AGTCAAATTCACAACGCGA
1 AGTCAAATTCGCAACGCGA
2107760 AACACAATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
19 2 0.02
20 101 0.96
21 2 0.02
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:2107896 original size:22 final size:22
Alignment explanation
Indices: 2107871--2107918 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
2107861 CTACGGTGAC
2107871 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
*
2107893 ATCCGTCTCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGGCGAA
2107915 ATCC
1 ATCC
2107919 ATCTATCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGGCGAA
Found at i:2108360 original size:14 final size:14
Alignment explanation
Indices: 2108338--2108369 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2108328 GCAATTTCAG
2108338 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
2108352 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
2108366 TTTC
1 TTTC
2108370 ATTTTTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:2110594 original size:42 final size:42
Alignment explanation
Indices: 2110547--2110663 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
2110537 GATGCATCTA
* *
2110547 TCATCATTCAAGAGGCGAC-TCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGC-ACATCCCACCGTTCAAGAGGCCCCTC
* * *
2110589 TCATCA-TCGAAGAAGCTCATCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCACATCCCACCGTTCAAGAGGCCCCTC
* * *
2110631 TCATCGTTCAAGAGGTCCCA-CCCGCCGTTCAAG
1 TCATCATTCAAGAGG-CACATCCCACCGTTCAAG
2110664 TGCCCGATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
41 3 0.05
42 54 0.87
43 5 0.08
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACATCCCACCGTTCAAGAGGCCCCTC
Found at i:2110638 original size:21 final size:21
Alignment explanation
Indices: 2110547--2110645 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
2110537 GATGCATCTA
* **
2110547 TCATCATTCAAGAGGCGACTC
1 TCATCGTTCAAGAGGCCCCTC
2110568 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * * *
2110589 TCATC-ATCGAAGAAGCTCATC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
2110610 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
2110631 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
2110646 TCCCACCCGC
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
20 3 0.05
21 52 0.90
22 3 0.05
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2112082 original size:69 final size:67
Alignment explanation
Indices: 2111995--2112167 Score: 194
Period size: 66 Copynumber: 2.6 Consensus size: 67
2111985 TGGGTACACT
*
2111995 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTATTTAA-TTGATAAGGAAATA
1 TTTTATTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTATTTAATTTGATAAGGAAATA
2112058 AGAATTA
61 AGAATTA
* * ** *
2112065 -TTTATTGTTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAAT
1 TTTTATTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTATTTAATTTGATAAGGAAATAAGAAT
2112128 TA
66 TA
* *
2112130 TTTTTTTGCTTATTTAATTG-ATTTGTAAAAGTTGATTT
1 TTTTATTGCTTGTTTAATTGAATTTGTAAAAGTTGATTT
2112168 GTTGTTTTAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
64 16 0.18
65 18 0.20
66 34 0.37
67 1 0.01
68 4 0.04
69 18 0.20
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.53
Consensus pattern (67 bp):
TTTTATTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTATTTAATTTGATAAGGAAATAAGAAT
TA
Found at i:2112113 original size:14 final size:13
Alignment explanation
Indices: 2112068--2112109 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2112058 AGAATTATTT
2112068 ATTG-TTTGTTTA
1 ATTGATTTGTTTA
**
2112080 ATTGATTTGTAAA
1 ATTGATTTGTTTA
2112093 AGTTGATTTGTTTA
1 A-TTGATTTGTTTA
2112107 ATT
1 ATT
2112110 TGATGTGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (13 bp):
ATTGATTTGTTTA
Found at i:2112124 original size:65 final size:65
Alignment explanation
Indices: 2112027--2112170 Score: 209
Period size: 66 Copynumber: 2.2 Consensus size: 65
2112017 TTTTACATTG
* * *
2112027 AAAGTTGATTTATTTAATTGATAAGGAAATAAGAATTA-TTTATTGTTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTATTTTATTGCTTATTTAATTGATTTGTA
** * *
2112091 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTATTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATAAGGAAATAAGAATTATTTTATTGCTTATTTAATTGATTTGT
2112156 A
65 A
2112157 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2112171 GTTTTAAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
64 16 0.23
65 18 0.25
66 37 0.52
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.51
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTATTTTATTGCTTATTTAATTGATTTGTA
Found at i:2112246 original size:20 final size:19
Alignment explanation
Indices: 2112217--2112259 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2112207 AAGACATGTT
* *
2112217 GAAAGTAAATTCGCAACGC
1 GAAAGTAAATTCACAACAC
2112236 GAAAGGTAAATTCACAACAC
1 GAAA-GTAAATTCACAACAC
2112256 GAAA
1 GAAA
2112260 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.14
Consensus pattern (19 bp):
GAAAGTAAATTCACAACAC
Found at i:2113346 original size:18 final size:18
Alignment explanation
Indices: 2113323--2113359 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2113313 CGAAATTTAT
2113323 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2113341 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2113359 A
1 A
2113360 CTCTAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2113773 original size:25 final size:25
Alignment explanation
Indices: 2113745--2113793 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2113735 CATTATTTTC
*
2113745 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2113770 CAAATAATGTACCCACAACAATGT
1 CAAATAATGTACCCACAACAATGT
2113794 AATTGATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2113906 original size:34 final size:34
Alignment explanation
Indices: 2113863--2113978 Score: 196
Period size: 34 Copynumber: 3.4 Consensus size: 34
2113853 AAGGTAAACT
*
2113863 TTCGCAACGCGAAATAAGCGTTGCGATAGTTAAA
1 TTCGCAACGCGAAATAAGCGTTGCGATAGTCAAA
2113897 TTCGCAACGCGAAATAAGCGTTGCGATAGTCAAA
1 TTCGCAACGCGAAATAAGCGTTGCGATAGTCAAA
* *
2113931 TTCGCAACTCGAAATAAGCATTGCGATAGTCAAA
1 TTCGCAACGCGAAATAAGCGTTGCGATAGTCAAA
*
2113965 TTCACAACGCGAAA
1 TTCGCAACGCGAAA
2113979 GTCAAATTCG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 77 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (34 bp):
TTCGCAACGCGAAATAAGCGTTGCGATAGTCAAA
Found at i:2116617 original size:24 final size:24
Alignment explanation
Indices: 2116583--2116636 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2116573 CCATCACATC
2116583 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2116607 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2116631 ATCAAA
1 ATCAAA
2116637 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2116650 original size:24 final size:24
Alignment explanation
Indices: 2116583--2116650 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2116573 CCATCACATC
* * *
2116583 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2116607 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2116631 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2116651 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2117412 original size:14 final size:15
Alignment explanation
Indices: 2117376--2117413 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2117366 GAAATCATTG
2117376 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2117391 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2117406 AAAAATTA
1 AAAAATTA
2117414 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2117593 original size:19 final size:19
Alignment explanation
Indices: 2117550--2117615 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
2117540 CAAAACATTT
* *
2117550 GTGTTGCGAAACTAAA-AC
1 GTGTTGCGAAATTAAATTC
*
2117568 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAATTAAATTC
*
2117587 GTGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAATTC
*
2117607 -AGTTGCGAA
1 GTGTTGCGAA
2117616 TTTGAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 14 0.35
19 20 0.50
20 6 0.15
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (19 bp):
GTGTTGCGAAATTAAATTC
Found at i:2117606 original size:20 final size:20
Alignment explanation
Indices: 2117569--2117699 Score: 117
Period size: 20 Copynumber: 6.6 Consensus size: 20
2117559 AACTAAAACC
*
2117569 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
2117588 TGTTGCGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTCG
*
2117607 AGTTGCGAATTTGAAATTTCG
1 TGTTGCGAATTTGAAA-TTCG
* * ** *
2117628 CGTTACGAATTTGACTTTTG
1 TGTTGCGAATTTGAAATTCG
*
2117648 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
*
2117668 TGTTGCG-ATTTACAAATTCG
1 TGTTGCGAATTT-GAAATTCG
*
2117688 CGTTGCGAATTT
1 TGTTGCGAATTT
2117700 TTTAATCATT
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
19 32 0.36
20 38 0.42
21 20 0.22
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:2130168 original size:30 final size:29
Alignment explanation
Indices: 2130134--2130190 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
2130124 AATTATACTA
*
2130134 ATATT-TAAATGATTATTTAAAAAATAAATG
1 ATATTCTAAAT-ATTAATT-AAAAATAAATG
*
2130164 ATATTCTTAATATTAATTAAAAATAAA
1 ATATTCTAAATATTAATTAAAAATAAA
2130191 AAATCAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 11 0.46
31 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (29 bp):
ATATTCTAAATATTAATTAAAAATAAATG
Found at i:2130495 original size:29 final size:29
Alignment explanation
Indices: 2130453--2130522 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
2130443 CTTCCCAGCA
2130453 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
2130482 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
2130511 TAGGTCGCCATG
1 TAGGTCGCCATG
2130523 GCGACCTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.14, C:0.33, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:2130526 original size:21 final size:21
Alignment explanation
Indices: 2130500--2130543 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2130490 CATGCACTCC
2130500 TGGCGACCTTGTAGGTCGCCA
1 TGGCGACCTTGTAGGTCGCCA
2130521 TGGCGACCTTGTAGGTCGCCA
1 TGGCGACCTTGTAGGTCGCCA
2130542 TG
1 TG
2130544 CACTCCTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.34, T:0.25
Consensus pattern (21 bp):
TGGCGACCTTGTAGGTCGCCA
Found at i:2130619 original size:14 final size:14
Alignment explanation
Indices: 2130597--2130632 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2130587 CCTCGCATAG
*
2130597 CTCGCTCGGATGCC
1 CTCGGTCGGATGCC
2130611 CTCGGTCGGATGCC
1 CTCGGTCGGATGCC
2130625 CTCGGTCG
1 CTCGGTCG
2130633 AATGGCTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.39, G:0.33, T:0.22
Consensus pattern (14 bp):
CTCGGTCGGATGCC
Found at i:2130643 original size:14 final size:14
Alignment explanation
Indices: 2130606--2130636 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2130596 GCTCGCTCGG
*
2130606 ATGCCCTCGGTCGG
1 ATGCCCTCGGTCGA
2130620 ATGCCCTCGGTCGA
1 ATGCCCTCGGTCGA
2130634 ATG
1 ATG
2130637 GCTTCGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.23
Consensus pattern (14 bp):
ATGCCCTCGGTCGA
Found at i:2131045 original size:29 final size:29
Alignment explanation
Indices: 2131003--2131108 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
2130993 CTTCCCAGCA
*
2131003 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
2131032 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
2131061 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
2131090 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
2131109 CCTGCTCCTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:2131201 original size:14 final size:14
Alignment explanation
Indices: 2131155--2131194 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
2131145 CCTCGCATAG
*
2131155 CTCGCTCGGATGCC
1 CTCGGTCGGATGCC
2131169 CTCGGTCGGATGCC
1 CTCGGTCGGATGCC
2131183 CTCGGTCGGATG
1 CTCGGTCGGATG
2131195 GCTTCGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.35, G:0.35, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGCC
Found at i:2131349 original size:558 final size:550
Alignment explanation
Indices: 2130303--2131410 Score: 2135
Period size: 558 Copynumber: 2.0 Consensus size: 550
2130293 ATTGAATAAT
2130303 GGCAAAATTTTCGAGATAATGTTCTCGAATTGTTTATTTAACGATATAACGTACTCCCAAGATTA
1 GGCAAAATTTTCGAGATAATGTTCTCGAATTGTTTATTTAACGATATAACGTACTCCCAAGATTA
2130368 ATTGCTCAAATAGGGCGAATTGCACAGTGTTGGCCGTAGGTCGCCATGCCTTCTGGGCGACCTAC
66 ATTGCTCAAATAGGGCGAATTGCACAGTGTTGGCCGTAGGTCGCCATGCCTTCTGGGCGACCTAC
2130433 GGCGTGGCAGCTTCCCAGCATAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACT
131 GGCGTGGCAGCTTCCCAGCATAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACT
2130498 CCTGGCGACCTTGTAGGTCGCCATGGCGACCTTGTAGGTCGCCATGCACTCCTCCTGCTCCTCGC
196 CCTGGCGACCTTGTAGGTCGCCATGGCGACCTTGTAGGTCGCCATGCACTCCTCCTGCTCCTCGC
2130563 GTGATTCCTCTTGCCCTCGGATGCCCTCGCATAGCTCGCTCGGATGCCCTCGGTCGGATGCCCTC
261 GTGATTCCTCTTGCCCTCGGATGCCCTCGCATAGCTCGCTCGGATGCCCTCGGTCGGATGCCCTC
2130628 GGTCGAATGGCTTCGGATGCCCAACGTGTTGGAACGTGCATGACACATGCAATCTCTCTCATAGC
326 GGTCGAATGGCTTCGGATGCCCAACGTGTTGGAACGTGCATGACACATGCAATCTCTCTCATAGC
2130693 TCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGATGGCATGACGACCTACGAGCAACACTG
391 TCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGATGGCATGACGACCTACGAGCAACACTG
2130758 TAGATTTCACCCTATTTGAGCAATTAATCTGAGGAGTGCATTATCTCGTGAATTAATTTATTCGA
456 TAGATTTCACCCTATTTGAGCAATTAATCTGAGGAGTGCATTATCTCGTGAATTAATTTATTCGA
2130823 GAACGTTATCTCGAGAGTTTAGCCATTGAA
521 GAACGTTATCTCGAGAGTTTAGCCATTGAA
2130853 GGCAAAATTTTCGAGATAATGTTCTCGAATTGTTTATTTAACGATATAACGTACTCCCAAGATTA
1 GGCAAAATTTTCGAGATAATGTTCTCGAATTGTTTATTTAACGATATAACGTACTCCCAAGATTA
2130918 ATTGCTCAAATAGGGCGAATTGCACAGTGTTGGCCGTAGGTCGCCATGCCTTCTGGGCGACCTAC
66 ATTGCTCAAATAGGGCGAATTGCACAGTGTTGGCCGTAGGTCGCCATGCCTTCTGGGCGACCTAC
2130983 GGCGTGGCAGCTTCCCAGCATAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACT
131 GGCGTGGCAGCTTCCCAGCATAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACT
2131048 CCTGGCGACCTTGTAGGTCGCCATGCACTCCTGGCGACCTTGTAGGTCGCCATGCACTCCTCCTG
196 CCTGGCGACCTTGTAGGTCG-C---CA----TGGCGACCTTGTAGGTCGCCATGCACTCCTCCTG
2131113 CTCCTCGCGTGATTCCTCTTGCCCTCGGATGCCCTCGCATAGCTCGCTCGGATGCCCTCGGTCGG
253 CTCCTCGCGTGATTCCTCTTGCCCTCGGATGCCCTCGCATAGCTCGCTCGGATGCCCTCGGTCGG
*
2131178 ATGCCCTCGGTCGGATGGCTTCGGATGCCCAACGTGTTGGAACGTGCATGACACATGCAATCTCT
318 ATGCCCTCGGTCGAATGGCTTCGGATGCCCAACGTGTTGGAACGTGCATGACACATGCAATCTCT
2131243 CTCATAGCTCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGATGGCATGACGACCTACGAG
383 CTCATAGCTCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGATGGCATGACGACCTACGAG
2131308 CAACACTGTAGATTTCACCCTATTTGAGCAATTAATCTGAGGAGTGCATTATCTCGTGAATTAAT
448 CAACACTGTAGATTTCACCCTATTTGAGCAATTAATCTGAGGAGTGCATTATCTCGTGAATTAAT
2131373 TTATTCGAGAACGTTATCTCGAGAGTTTAGCCATTGAA
513 TTATTCGAGAACGTTATCTCGAGAGTTTAGCCATTGAA
2131411 TAATACTTTG
Statistics
Matches: 549, Mismatches: 1, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
550 215 0.39
551 1 0.00
554 2 0.00
558 331 0.60
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.26
Consensus pattern (550 bp):
GGCAAAATTTTCGAGATAATGTTCTCGAATTGTTTATTTAACGATATAACGTACTCCCAAGATTA
ATTGCTCAAATAGGGCGAATTGCACAGTGTTGGCCGTAGGTCGCCATGCCTTCTGGGCGACCTAC
GGCGTGGCAGCTTCCCAGCATAGGTCGCCATGCACTCCGGGCGACCTTGTAGGTCGCCATGCACT
CCTGGCGACCTTGTAGGTCGCCATGGCGACCTTGTAGGTCGCCATGCACTCCTCCTGCTCCTCGC
GTGATTCCTCTTGCCCTCGGATGCCCTCGCATAGCTCGCTCGGATGCCCTCGGTCGGATGCCCTC
GGTCGAATGGCTTCGGATGCCCAACGTGTTGGAACGTGCATGACACATGCAATCTCTCTCATAGC
TCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGATGGCATGACGACCTACGAGCAACACTG
TAGATTTCACCCTATTTGAGCAATTAATCTGAGGAGTGCATTATCTCGTGAATTAATTTATTCGA
GAACGTTATCTCGAGAGTTTAGCCATTGAA
Found at i:2140194 original size:29 final size:29
Alignment explanation
Indices: 2140152--2140207 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
2140142 GGTTTTATGC
2140152 GGGTAAAAGAATTGAATGTTAGAGCGAGA
1 GGGTAAAAGAATTGAATGTTAGAGCGAGA
2140181 GGGTAAAAGAATTGAATGTTAGAGCGA
1 GGGTAAAAGAATTGAATGTTAGAGCGA
2140208 ACCGTGGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.34, T:0.21
Consensus pattern (29 bp):
GGGTAAAAGAATTGAATGTTAGAGCGAGA
Found at i:2140356 original size:14 final size:14
Alignment explanation
Indices: 2140337--2140372 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2140327 TGTTCTATTA
2140337 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
2140351 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
2140365 TATGTTCG
1 TATGTTCG
2140373 AACATAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.19, T:0.56
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:2140655 original size:14 final size:14
Alignment explanation
Indices: 2140636--2140668 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2140626 TGTTTGTGTT
2140636 GTTTATTTATATTC
1 GTTTATTTATATTC
*
2140650 GTTTA-TTGTATTC
1 GTTTATTTATATTC
2140663 GTTTAT
1 GTTTAT
2140669 GTTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.64
Consensus pattern (14 bp):
GTTTATTTATATTC
Found at i:2140667 original size:23 final size:23
Alignment explanation
Indices: 2140641--2140725 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
2140631 GTGTTGTTTA
* *
2140641 TTTATATTCGTTTATTGTATTCG
1 TTTATGTTCGTTTATTGTGTTCG
** *
2140664 TTTATGTTTATTTATTATGTTCG
1 TTTATGTTCGTTTATTGTGTTCG
*
2140687 TTTATGTTCGCTCGT-TTGTGTTCG
1 TTTATGTTCG-T-TTATTGTGTTCG
2140711 TTTATGTTCGTTTAT
1 TTTATGTTCGTTTAT
2140726 CATTTAAATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
22 1 0.02
23 28 0.57
24 19 0.39
25 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTATGTTCGTTTATTGTGTTCG
Found at i:2140675 original size:14 final size:13
Alignment explanation
Indices: 2140636--2140675 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
2140626 TGTTTGTGTT
2140636 GTTTATTTATATTC
1 GTTTATTT-TATTC
*
2140650 GTTTATTGTATTC
1 GTTTATTTTATTC
2140663 GTTTATGTTTATT
1 GTTTAT-TTTATT
2140676 TATTATGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.65
Consensus pattern (13 bp):
GTTTATTTTATTC
Found at i:2140691 original size:10 final size:10
Alignment explanation
Indices: 2140678--2140725 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
2140668 TGTTTATTTA
2140678 TTATGTTCGT
1 TTATGTTCGT
2140688 TTATGTTCGCTCGT
1 TTATG-T---TCGT
*
2140702 TTGTGTTCGT
1 TTATGTTCGT
2140712 TTATGTTCGT
1 TTATGTTCGT
2140722 TTAT
1 TTAT
2140726 CATTTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 22 0.69
11 1 0.03
13 1 0.03
14 8 0.25
ACGTcount: A:0.08, C:0.12, G:0.21, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:2142299 original size:32 final size:27
Alignment explanation
Indices: 2142237--2142293 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2142227 TGTTTGGGTA
2142237 GGTTTTTTAAGTGTGATATTCGGGTCG
1 GGTTTTTTAAGTGTGATATTCGGGTCG
*
2142264 GGTTTTTTAAGTGTGATATTCAGGTCG
1 GGTTTTTTAAGTGTGATATTCGGGTCG
2142291 GGT
1 GGT
2142294 CGGGTTCGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.16, C:0.07, G:0.33, T:0.44
Consensus pattern (27 bp):
GGTTTTTTAAGTGTGATATTCGGGTCG
Found at i:2142477 original size:281 final size:274
Alignment explanation
Indices: 2141981--2142485 Score: 730
Period size: 281 Copynumber: 1.8 Consensus size: 274
2141971 TTTTTATTAT
* * *
2141981 TTCGGGTCGGGTTTTTAATTCATATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAATA
1 TTCGGGTCGGGTTTTTAAGTCATATATTCAGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAATA
* * * *
2142046 CTCGACCCGAAAATAAATATAATTTTATCATATATATTTAGGAATAATTATAATAATAACCCTCT
66 CTCGACCCGAAAAAAAATATAATTTTACCATATATATTTAGAAATAATTACAATAATAACCCTCT
* * * *
2142111 ATATATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTTTATTATTTCG
131 ATATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCA
2142176 GGTCAGGTCGGATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGTTTGGGTAGGTT
196 GGTCAGGTCGGATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGTTTGGGTAGGTT
2142241 TTTTAAGTGTGATA
261 TTTTAAGTGTGATA
* *
2142255 TTCGGGTCGGGTTTTTTAAGT-GTGATATTCAGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAA
1 TTCGGGTCGGG-TTTTTAAGTCAT-ATATTCAGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAA
*
2142319 -AC-CGGACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACAATAATA
64 TACTC-GACCCGA---AAAAAA-ATATAATTTTACCATATATATTTAGAAATAATTACAATAATA
*
2142382 CCCCTCTATATATAATTTTTTTTCCCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTT
124 ACCCTCTATATATAA-TTTTTTT--CAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTT
* *
2142447 TATTATTTTATGTC-GTGTCGGATTTCTAATTCATATATT
186 TATTATTTCAGGTCAG-GTCGGATTTCTAATTCATATATT
2142486 GAATAAAAAT
Statistics
Matches: 203, Mismatches: 17, Indels: 15
0.86 0.07 0.06
Matches are distributed among these distances:
273 1 0.00
274 21 0.10
275 45 0.22
277 5 0.02
278 52 0.26
279 7 0.03
280 1 0.00
281 71 0.35
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (274 bp):
TTCGGGTCGGGTTTTTAAGTCATATATTCAGGTCGGGTCGAGTTCGAGTTTAGGGTGAAAAAATA
CTCGACCCGAAAAAAAATATAATTTTACCATATATATTTAGAAATAATTACAATAATAACCCTCT
ATATATAATTTTTTTCAATTAAATCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCA
GGTCAGGTCGGATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGTTTGGGTAGGTT
TTTTAAGTGTGATA
Found at i:2163972 original size:20 final size:20
Alignment explanation
Indices: 2163947--2163984 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2163937 TTTTGGTGCA
*
2163947 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
2163967 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
2163985 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2166301 original size:25 final size:25
Alignment explanation
Indices: 2166273--2166400 Score: 145
Period size: 25 Copynumber: 5.6 Consensus size: 25
2166263 AACAAAAAGG
2166273 GGGAGAAGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTTAAATGTTTTAAAT
2166298 GGGAGAAGTGTTAAA-G---T-AA-
1 GGGAGAAGTGTTAAATGTTTTAAAT
*
2166317 GGGGGAAGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTTAAATGTTTTAAAT
*
2166342 AGGAGAAGTGTTAAA-G---T-AA-
1 GGGAGAAGTGTTAAATGTTTTAAAT
*
2166361 GGGGGAAGTGTTAAATGTTTTAAAT
1 GGGAGAAGTGTTAAATGTTTTAAAT
2166386 GGGAGAAGTGTTAAA
1 GGGAGAAGTGTTAAA
2166401 GTAAGGGGGA
Statistics
Matches: 85, Mismatches: 6, Indels: 24
0.74 0.05 0.21
Matches are distributed among these distances:
19 27 0.32
20 6 0.07
21 2 0.02
23 2 0.02
24 6 0.07
25 42 0.49
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.30
Consensus pattern (25 bp):
GGGAGAAGTGTTAAATGTTTTAAAT
Found at i:2166326 original size:19 final size:19
Alignment explanation
Indices: 2166302--2166410 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
2166292 TTAAATGGGA
2166302 GAAGTGTTAAAGTAAGGGG
1 GAAGTGTTAAAGTAAGGGG
* *
2166321 GAAGTGTTAAATGTTTTAAATAGGA
1 GAAGTGTTAAA-G---T-AA-GGGG
2166346 GAAGTGTTAAAGTAAGGGG
1 GAAGTGTTAAAGTAAGGGG
*
2166365 GAAGTGTTAAATGTTTTAAATGGGA
1 GAAGTGTTAAA-G---T-AA-GGGG
2166390 GAAGTGTTAAAGTAAGGGG
1 GAAGTGTTAAAGTAAGGGG
2166409 GA
1 GA
2166411 GTAATTTTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 24
0.71 0.06 0.24
Matches are distributed among these distances:
19 29 0.40
20 6 0.08
21 2 0.03
23 2 0.03
24 6 0.08
25 27 0.38
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.28
Consensus pattern (19 bp):
GAAGTGTTAAAGTAAGGGG
Found at i:2166328 original size:44 final size:44
Alignment explanation
Indices: 2166272--2166410 Score: 260
Period size: 44 Copynumber: 3.1 Consensus size: 44
2166262 TAACAAAAAG
2166272 GGGGAGAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
1 GGGG-GAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
*
2166317 GGGGGAAGTGTTAAATGTTTTAAATAGGAGAAGTGTTAAAGTAA
1 GGGGGAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
2166361 GGGGGAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
1 GGGGGAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
2166405 GGGGGA
1 GGGGGA
2166411 GTAATTTTTC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
44 88 0.96
45 4 0.04
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.28
Consensus pattern (44 bp):
GGGGGAAGTGTTAAATGTTTTAAATGGGAGAAGTGTTAAAGTAA
Found at i:2166840 original size:21 final size:21
Alignment explanation
Indices: 2166816--2166869 Score: 101
Period size: 20 Copynumber: 2.6 Consensus size: 21
2166806 CTCGGAGGGA
2166816 ACCGATTCCCCCCTAGGGGGT
1 ACCGATTCCCCCCTAGGGGGT
2166837 ACCGATT-CCCCCTAGGGGGT
1 ACCGATTCCCCCCTAGGGGGT
2166857 ACCGATTCCCCCC
1 ACCGATTCCCCCC
2166870 ACTGTTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.15, C:0.43, G:0.24, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCCCTAGGGGGT
Found at i:2169442 original size:59 final size:58
Alignment explanation
Indices: 2169349--2169464 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 58
2169339 AGTTGGCAAT
** * *
2169349 GCGTTGAGGCCCCTCACTTTTGATTATCTTCAAGTGGTTTCTTCGGTTTGACGTTTCGA
1 GCGTTGAGGCCCCTCACTTTTGATTATCCACAAGTGGTTAC-ACGGTTTGACGTTTCGA
2169408 GCGTTGAGGCCCCTCACTTTTGATTATCCACAAGTGGTTACACGGTTTGACGTTTCG
1 GCGTTGAGGCCCCTCACTTTTGATTATCCACAAGTGGTTACACGGTTTGACGTTTCG
2169465 GTTGCTCGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 15 0.28
59 38 0.72
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (58 bp):
GCGTTGAGGCCCCTCACTTTTGATTATCCACAAGTGGTTACACGGTTTGACGTTTCGA
Found at i:2169791 original size:18 final size:18
Alignment explanation
Indices: 2169765--2169801 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2169755 CCTGTGAATT
*
2169765 ATATTACTAATGTTTGTA
1 ATATAACTAATGTTTGTA
2169783 ATATAACTAATGTTTGTA
1 ATATAACTAATGTTTGTA
2169801 A
1 A
2169802 CTCTTGGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (18 bp):
ATATAACTAATGTTTGTA
Found at i:2172150 original size:11 final size:12
Alignment explanation
Indices: 2172134--2172162 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2172124 GACACTTTAA
2172134 TATTAT-GATTT
1 TATTATGGATTT
2172145 TATTATGGATTT
1 TATTATGGATTT
2172157 TATTAT
1 TATTAT
2172163 TCTAGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TATTATGGATTT
Found at i:2172180 original size:75 final size:73
Alignment explanation
Indices: 2172082--2172295 Score: 197
Period size: 75 Copynumber: 2.9 Consensus size: 73
2172072 TTGAGTTTAA
* * *
2172082 TATTTTTCTAGACTTAATATTATGGTTTAAGTCTTAAGATTTGACACTTTAATATTATGATTTTA
1 TATTATTCTAGAATTAATATTATGGTTTAAGTCTTAAAATTTGACA-TTTAATATTATGATTTT-
2172147 TTATGGATTT
64 TTATGGATTT
* * *
2172157 TATTATTCTAGAATTAATATTATGGTTTGAA-TATTAAAATTTGATATTTTAATATTGTTG-TTT
1 TATTATTCTAGAATTAATATTATGGTTT-AAGTCTTAAAATTTGACA-TTTAATATT-ATGATTT
2172220 GTTTATGGATTT
63 -TTTATGGATTT
* * * * * * * *
2172232 TACTGTTATA-AACTTAATATTGTTGTTTGAGTCTTGATATTTGACA-TT-AT-TTATGATTTTT
1 TATTATTCTAGAA-TTAATATTATGGTTTAAGTCTTAAAATTTGACATTTAATATTATGATTTTT
2172293 TAT
65 TAT
2172296 ATATATTTAT
Statistics
Matches: 115, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
70 7 0.06
71 5 0.04
72 2 0.02
73 2 0.02
74 3 0.03
75 91 0.79
76 5 0.04
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.54
Consensus pattern (73 bp):
TATTATTCTAGAATTAATATTATGGTTTAAGTCTTAAAATTTGACATTTAATATTATGATTTTTT
ATGGATTT
Found at i:2181197 original size:58 final size:58
Alignment explanation
Indices: 2181107--2181221 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
2181097 AGGTTTATAT
2181107 AGAGATAAGAAGCAACCCAAAGTGGCTTACTTTTATTCCTTTTTTCCCCAACCTTTCG
1 AGAGATAAGAAGCAACCCAAAGTGGCTTACTTTTATTCCTTTTTTCCCCAACCTTTCG
2181165 AGAGATAAGAAGCAACCCAAAGTGGCTTACTTTTATTCCTTTTTTCCCCAACCTTTC
1 AGAGATAAGAAGCAACCCAAAGTGGCTTACTTTTATTCCTTTTTTCCCCAACCTTTC
2181222 ATGGTTGAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (58 bp):
AGAGATAAGAAGCAACCCAAAGTGGCTTACTTTTATTCCTTTTTTCCCCAACCTTTCG
Found at i:2182759 original size:17 final size:19
Alignment explanation
Indices: 2182719--2182767 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
2182709 ATGTTCAGGT
2182719 TTTTTAAAAAATATATATA
1 TTTTTAAAAAATATATATA
* *
2182738 TTTTTAAATAATAT-TTTA
1 TTTTTAAAAAATATATATA
2182756 -TTTTAAAAAATA
1 TTTTTAAAAAATA
2182768 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 11 0.41
18 3 0.11
19 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAAAAAATATATATA
Found at i:2186937 original size:15 final size:15
Alignment explanation
Indices: 2186896--2186939 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 15
2186886 ATACATAGTC
2186896 TCTTAATCATTCAGG
1 TCTTAATCATTCAGG
2186911 TCATTGAATCATTCAGCG
1 TC-TT-AATCATTCAG-G
2186929 -CTTAATCATTC
1 TCTTAATCATTC
2186940 TGAAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 11 0.42
18 1 0.04
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (15 bp):
TCTTAATCATTCAGG
Found at i:2190648 original size:32 final size:32
Alignment explanation
Indices: 2190612--2190675 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2190602 ACTGCTGTTA
2190612 ATTTTTAACGTAGATGATAACATGTATGACAT
1 ATTTTTAACGTAGATGATAACATGTATGACAT
2190644 ATTTTTAACGTAGATGATAACATGTATGACAT
1 ATTTTTAACGTAGATGATAACATGTATGACAT
2190676 GTATGTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (32 bp):
ATTTTTAACGTAGATGATAACATGTATGACAT
Found at i:2190713 original size:12 final size:13
Alignment explanation
Indices: 2190696--2190725 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2190686 GAAATTCTCA
2190696 TAATTATAT-ATT
1 TAATTATATAATT
2190708 TAATTATATAATT
1 TAATTATATAATT
2190721 TAATT
1 TAATT
2190726 TTTAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATTATATAATT
Found at i:2190867 original size:23 final size:24
Alignment explanation
Indices: 2190832--2190877 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2190822 GAAGAATTAA
2190832 TTTAATTAGTTTAAATT-AATAAAT
1 TTTAATTAGTTT-AATTAAATAAAT
*
2190856 TTTAA-TATTTTAATTAAATAAA
1 TTTAATTAGTTTAATTAAATAAA
2190878 CATTGAGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 11 0.55
24 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAATTAGTTTAATTAAATAAAT
Found at i:2191344 original size:2 final size:2
Alignment explanation
Indices: 2191337--2191374 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2191327 TATAATTTAA
* *
2191337 AT AT AT AT AC AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2191375 GAAATAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2216158 original size:18 final size:18
Alignment explanation
Indices: 2216135--2216170 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2216125 TTGTCAAGTA
2216135 TTGAGGAGAAAAAGACAG
1 TTGAGGAGAAAAAGACAG
*
2216153 TTGAGGAGAAGAAGACAG
1 TTGAGGAGAAAAAGACAG
2216171 CTAAGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.36, T:0.11
Consensus pattern (18 bp):
TTGAGGAGAAAAAGACAG
Done.